4N7H

Crystal Structure of the Complex of 3rd WW domain of Human Nedd4 and 1st PPXY Motif of ARRDC3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.698 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and biochemical basis for ubiquitin ligase recruitment by arrestin-related domain-containing protein-3 (ARRDC3).

Qi, S.O'Hayre, M.Gutkind, J.S.Hurley, J.H.

(2014) J.Biol.Chem. 289: 4743-4752

  • DOI: 10.1074/jbc.M113.527473
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • After protracted stimulation, the β2-adrenergic receptor and many other G-protein-coupled receptors are ubiquitinated and down-regulated. Arrestin-related domain-containing protein-3 (ARRDC3) has been proposed to recruit the ubiquitin ligase Nedd4 to ...

    After protracted stimulation, the β2-adrenergic receptor and many other G-protein-coupled receptors are ubiquitinated and down-regulated. Arrestin-related domain-containing protein-3 (ARRDC3) has been proposed to recruit the ubiquitin ligase Nedd4 to the β2-adrenergic receptor. ARRDC3 contains two PPXY motifs that could potentially interact with any of the four WW domains of Nedd4. Here we dissect the interaction determinants. ARRDC3 PPXY-Nedd4 WW dissociation constants vary from unmeasurable to Kd = 3 μM for the third WW domain of Nedd4 binding to the first PPXY motif of ARRDC3. Structures of the uncomplexed and PPXY1-bound WW3 domain were determined at 1.1 and 1.7 Å resolution. The structures revealed conformational changes upon binding and the hydrogen bonding network in exquisite detail. Tight packing of ARRDC3 Val-352', part of a 310 helix at the C terminus of PPXY1, is important for high affinity binding to WW3. Although no single WW domain is strictly essential for the binding of Nedd4 and ARRDC3 expressed in HEK293 cells, high affinity binding of full-length ARRDC3 and Nedd4 is driven by the avid interaction of both PPXY motifs with either the WW2-WW3 or WW3-WW4 combinations, with Kd values as low as 300 nM.


    Organizational Affiliation

    From the Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California 94720 and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase NEDD4
A
37Homo sapiensMutation(s): 0 
Gene Names: NEDD4 (KIAA0093, NEDD4-1)
EC: 2.3.2.26
Find proteins for P46934 (Homo sapiens)
Go to Gene View: NEDD4
Go to UniProtKB:  P46934
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Arrestin domain-containing protein 3
B
13Homo sapiensMutation(s): 0 
Gene Names: ARRDC3 (KIAA1376)
Find proteins for Q96B67 (Homo sapiens)
Go to Gene View: ARRDC3
Go to UniProtKB:  Q96B67
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAI
Query on GAI

Download SDF File 
Download CCD File 
A
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.698 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 38.882α = 90.00
b = 38.882β = 90.00
c = 49.997γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references
  • Version 1.2: 2014-10-08
    Type: Database references